Ha, I never heard of any textbooks gain significant popularity either. I guess reading textbooks attracts audience with low motivation.
In seriousness though why do you think any educational game would ever gain popularity anywhere close to popular video games.And what the popularity of the material even have to do with the motivation of its consumers???
There are (used to be?) widely recommended books for certain topics, such as K&R's "The C Programming Language". I don't think any programming games are anywhere near the popularity of these books.
I think CodeCombat is pretty widely recommended specifically for teaching coding to kids. Not sure if it counts -- it's more coding lessons that are gamified in overall structure, and also the lessons themselves have gaming aesthetics (e.g. "Write code to move your hero to kill these orcs and open treasure chests").
There's a ton of resources for this area now though, I'm not sure I can point to any one thing as a standard.
In seriousness though why do you think any educational game would ever gain popularity anywhere close to popular video games.And what the popularity of the material even have to do with the motivation of its consumers???